Hi Cengiz Kaan Ferah,
you might want to look at
Successful sample preparation for serial crystallography experiments
https://pmc.ncbi.nlm.nih.gov/articles/PMC6878878/
And I just stumbled about this one
https://www.nature.com/articles/s41596-022-00777-5 (not yet read)
Br, Georg.
Am 2025-0
Hi, here a script you can use in a jupyter notebook or colab:
!pip install biopython
importos
importrequests
fromBio importPDB
importshutil
fromgoogle.colab importfiles
# Create the folder if it doesn't exist
ifnotos.path.exists('pdb_files'):
os.makedirs('pdb_files')
# Function to download PD
Dear Stuart,
you have to add
allow_duplicate_sequence_numbers()
to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was
Dear Pavel,
I guess you know that Billy made cctbx "available" on colab. So
installing cctbx and python is not needed any more.
https://github.com/phenix-project/Colabs/blob/main/Start_cctbx.ipynb
There are also some descriptions of some modifications to
the installation so that everything w
Dear Yong, please have a look at this
https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/tutorial/index_en.html
You get even the raw data, but also all files in between till the fully
refined structure.
It covers MR, SAD , .
I know it is CCP4 mailing list, but
Dear Paul,
can you please tell me what the Acedrg Tables reference (I assume a
table of curated stereochemistry values) and where I can find that table?
Where does coot save these cif files? (Not in
CCP4-7\7.1\Lib\data\monomers\ as I always thought, before I tried now.)
Many thanks, br Geo
Hi,
hard evidence I could not find. I once cited "An approach to
crystallizing proteins by synthetic symmetrization" for a publication on
a rescue strategy in crystallization.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/
They reference to a Phd thesis from 2003.
And one idea why it
Dear Harry, you can run alphafold via
https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb#scrollTo=woIxeCPygt7K
*Cited*
*"Differences to AlphaFold v2.0*
In comparison to AlphaFold v2.0, this Colab notebook uses*no templates
(homologous structures)*a
Hi Jack, was the dewar shipped on 1st April and just arrived? You can
buy the CX100 also as CXR100 and there you can replace the adsorbent
material. Looks like this.
https://www.google.com/search?q=replaceable+adsorbent+material+kits&rlz=1C1CHBF_deAT848AT848&sxsrf=ALeKk01N9aWj7Kw07AMDN1oGMnke1s
Dear Jesus, you should look at
https://www.rappsilberlab.org/software/
or
https://www.maxquant.org/
Altough there have been huge strides in recent years in software
development, XL-MS data processing need still some effort.
Br, Georg.
Am 2020-06-08 um 9:48 AM schrieb JESUS BALTANAS COPADO:
Hi Sergei, this publication should be useful for you.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756611/
Additionally it is proposed that when your protein is not so stable
(lower Tm), one should incubate the screens at 4C.
http://scripts.iucr.org/cgi-bin/paper?S0907444911036225
Br, Georg
Dear Guenter, yes look at crambin (pdbcode 1EJG).
This crashes Coot until you add*
allow_duplicate_sequence_numbers()
to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these
Dear All, asking a few years back the question why phasing power is not
reported, I got following answer:
No, we don't generate phasing power statistics in Phaser, just the
figures of merit, which usually give a good indication of how well
things have worked. Phasing power is defined in terms
Dear all, I am considering to buy a new laptop and would like to install
the latest ubuntu version and have 3D glasses. Following the discussions
in the lasts years, this issue seems to be not trivial. Which setup of
laptop and 3D glasses will work plug and play?
And what about VR. When is coo
If you buy a used one, or the one from Biobase China make a quality
check before. Loosing crystals during shipment means loosing money
(accounting for all the efforts that went in producing the crystals).
I once got a protocol from Terese Bergfors at Uppsala University". It
consists of what T
Dear Frank,
pdb_redo webserver does. However you have to cheat to provoke it: The
resolution remark in the PDB has to be 0.10A beyond what it was used
before. You can use also use the command line version of pdb-redo to
tweak settings for your calculation (the expert option).
However it woul
Dear Nicola,
Extensions --> Modelling --> Copy Fragment
Then Edit --> Merge Molecules
Br, Georg.
On 2018-10-08 10:24, Nicola Evans wrote:
A while back I was shown in Coot how to take a ligand from one PDB and insert
it into another one - this is really useful if you have superimposed a
hom
Dear Gloria,
probably even when you make the protein synthetically there will be
proteases in your solution, because many "air allergens" are proteases
(The major HDM allergens (i.e., allergens recognized by the majority of
HDM allergic subjects) are present in high amounts in the fecal pellet
Dear Chandra, we are also currently getting quotes for a new microscope.
I recently worked at Oak ridge with a Zeiss SteREO Discovery.V20
https://www.zeiss.com/microscopy/us/products/stereo-zoom-microscopes/stereo-discovery-v20.html
(everything motorized, which is not really needed) and at diamo
Dear Kay, thank you ver much for the (as always) detailed and nicely
explained answer.
However this brings up some questions for me:
1. Could you please tell me how the "correct high-resolution cutoff"
will effect the data processing in the INTEGRATE CORRECT step.
In other words what will be
Hi Tarun,
Carsten is right the Proteum2 software is really good. I can send you
some introduction pdfs and for SADABS (scaling) I am currently writing
an SOP, the manual is also well written.
Besides this the program to unwarp and convert images, is in the
instrument tab.
Best regards, G
Hi Xiao, you can also download from pdb_redo
http://www.cmbi.ru.nl/pdb_redo/ if a rerefined, updated and optimized
X-ray structure model is also ok for you. Depends what your intentions are.
Best regards, Georg.
On 06/09/2015 11:02 PM, Pavel Afonine wrote:
Hi Xiao,
just calculate it yourself
Dear George and Phil, thanks a lot for the fast answers. Things are
unfortunately a bit more complicated and the usually very convenient way using
SAINT-SADABS-XPREP has too much limitations for this datasets because
1. It starts with that one datasets has more than 2.000.000 reflections (space
Dear Colleagues,
After reading a few papers about growing suitable crystals for neutron
diffraction. I will do capillary counterdiffusion with an agarose plug
between mother liquor and protein solution like described in
http://www.ncbi.nlm.nih.gov/pubmed/23192028.
However I looked quite som
if somebody could point me in the direction where the
problem is or show me an alternative route.
Best regards Georg.
--
Mlynek Georg
University of Vienna
Department of Computational and Structural Biology Max F. Perutz Laboratories
Campus Vienna Biocenter 5 level -2
1030 Vienna Austria
e-ma
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